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- PDB-6f4r: Human JMJD5 (N308C) in complex with Mn(II), NOG and RCCD1 (139-14... -

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Basic information

Entry
Database: PDB / ID: 6f4r
TitleHuman JMJD5 (N308C) in complex with Mn(II), NOG and RCCD1 (139-143) (complex-3)
Components
  • JmjC domain-containing protein 5
  • RCC1 domain-containing protein 1
KeywordsOXIDOREDUCTASE / NON-HEME / IRON / 2-OXOGLUTARATE / DIOXYGENASE / JMJC / JMJC DOMAIN / Lysine-specific demethylase 8 / JmjC domain-containing protein 5 / Arginyl C-3 Hydroxylase / JMJD5 / KDM8 / OXYGENASE / HYPOXIA / DNA-BINDING / METAL-BINDING / TRANSLATION / DSBH / FACIAL TRIAD / CYTOPLASM / JMJC HYDROXYLASE / JMJC DEMETHYLASE / KDMS / POST-TRANSLATIONAL MODIFICATIONS / PTM / BETA-HYDROXYLATION / HYDROXYLATION / ARGININE HYDROXYLATION / RCC1 domain-containing protein 1 / RCCD1 / Regulator of chromosome condensation / 40S ribosomal protein S6 / RPS6 / RIBOSOME BIOGENESIS / TRANSCRIPTION / EPIGENETIC REGULATION / SIGNALING / DEVELOPMENT / CELL STRUCTURE / TRANSCRIPTION ACTIVATOR/INHIBITOR / PHOSPHORYLATION / CANCER / POLYMORPHISM
Function / homology
Function and homology information


[protein]-arginine 3-hydroxylase / peptidyl-arginine 3-dioxygenase activity / histone H3K36 demethylase activity / Hydrolases; Acting on peptide bonds (peptidases) / Protein hydroxylation / aminopeptidase activity / : / regulation of signal transduction by p53 class mediator / circadian regulation of gene expression / protein destabilization ...[protein]-arginine 3-hydroxylase / peptidyl-arginine 3-dioxygenase activity / histone H3K36 demethylase activity / Hydrolases; Acting on peptide bonds (peptidases) / Protein hydroxylation / aminopeptidase activity / : / regulation of signal transduction by p53 class mediator / circadian regulation of gene expression / protein destabilization / G2/M transition of mitotic cell cycle / p53 binding / chromatin organization / chromosome / fibroblast proliferation / endopeptidase activity / in utero embryonic development / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of DNA-templated transcription / proteolysis / nucleoplasm / metal ion binding / nucleus / plasma membrane / cytosol
Similarity search - Function
: / : / KDM8-like, N-terminal ARM repeats / Regulator of chromosome condensation (RCC1) signature 2. / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation, RCC1 / Regulator of chromosome condensation (RCC1) repeat profile. / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / Cupin-like domain 8 / Cupin-like domain ...: / : / KDM8-like, N-terminal ARM repeats / Regulator of chromosome condensation (RCC1) signature 2. / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation, RCC1 / Regulator of chromosome condensation (RCC1) repeat profile. / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / Cupin-like domain 8 / Cupin-like domain / Cupin / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / N-OXALYLGLYCINE / RCC1 domain-containing protein 1 / Bifunctional peptidase and arginyl-hydroxylase JMJD5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsChowdhury, R. / Islam, M.S. / Schofield, C.J.
CitationJournal: Nat Commun / Year: 2018
Title: JMJD5 is a human arginyl C-3 hydroxylase.
Authors: Wilkins, S.E. / Islam, S. / Gannon, J.M. / Markolovic, S. / Hopkinson, R.J. / Ge, W. / Schofield, C.J. / Chowdhury, R.
History
DepositionNov 30, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 4, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2019Group: Data collection / Structure summary
Category: audit_author / database_PDB_rev / database_PDB_rev_record
Item: _audit_author.name
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: JmjC domain-containing protein 5
B: RCC1 domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3875
Polymers30,0632
Non-polymers3243
Water6,485360
1
A: JmjC domain-containing protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8034
Polymers29,4791
Non-polymers3243
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RCC1 domain-containing protein 1


  • defined by author
  • 584 Da, 1 polymers
Theoretical massNumber of molelcules
Total (without water)5841
Polymers5841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.429, 64.810, 77.982
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein JmjC domain-containing protein 5 / Jumonji domain-containing protein 5 / Lysine-specific demethylase 8


Mass: 29479.135 Da / Num. of mol.: 1 / Mutation: C217A, C232A, C295A, N308C, C384A
Source method: isolated from a genetically manipulated source
Details: CATALYTIC DOMAIN (RESIDUES 183-416) / Source: (gene. exp.) Homo sapiens (human) / Gene: KDM8, JMJD5 / Plasmid: PNIC28 BSA4 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q8N371, [50S ribosomal protein L16]-arginine 3-hydroxylase
#2: Protein/peptide RCC1 domain-containing protein 1


Mass: 583.681 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: FRAGMENT: 139-143 / Source: (synth.) Homo sapiens (human) / References: UniProt: A6NED2

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Non-polymers , 4 types, 363 molecules

#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-OGA / N-OXALYLGLYCINE


Mass: 147.086 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H5NO5 / Comment: inhibitor*YM
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 360 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: 0.1M Bis-Tris pH 5.8, 25 % PEG3350, 0.002 M MnCl2, 300 nl sitting drops (sample:well, 1:1 ratio)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 19, 2016 / Details: MIRRORS
RadiationCollimation: MIRRORS / Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.3→49.84 Å / Num. obs: 62115 / % possible obs: 100 % / Redundancy: 9 % / Biso Wilson estimate: 15.5 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.031 / Net I/σ(I): 24.3
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 8.8 % / Rmerge(I) obs: 1.2 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 6098 / CC1/2: 0.568 / Rpim(I) all: 0.553 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000706Edata reduction
HKL-2000706Edata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6F4P

6f4p


Resolution: 1.3→49.84 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 15.5 / Stereochemistry target values: ML
Details: REFINEMENT TARGET : ML and BULK SOLVENT MODELLING METHOD USED: FLAT MODEL
RfactorNum. reflection% reflectionSelection details
Rfree0.1616 3045 4.91 %Random
Rwork0.1427 ---
obs0.1436 62039 98.89 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT MODEL / Bsol: 54.2 Å2 / ksol: 0.41 e/Å3
Displacement parametersBiso mean: 24 Å2
Baniso -1Baniso -2Baniso -3
1--1.91 Å20 Å20 Å2
2---0.52 Å20 Å2
3---2.43 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.16 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a-0.16 Å
Refinement stepCycle: LAST / Resolution: 1.3→49.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1939 0 19 360 2318
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0162345
X-RAY DIFFRACTIONf_angle_d1.4013232
X-RAY DIFFRACTIONf_dihedral_angle_d15.683886
X-RAY DIFFRACTIONf_chiral_restr0.1330
X-RAY DIFFRACTIONf_plane_restr0.011438
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2968-1.31710.28721010.27152005X-RAY DIFFRACTION76
1.3171-1.33870.31071310.24932715X-RAY DIFFRACTION100
1.3387-1.36180.26261430.24072648X-RAY DIFFRACTION100
1.3618-1.38650.21551330.23072676X-RAY DIFFRACTION100
1.3865-1.41320.23511390.21322688X-RAY DIFFRACTION100
1.4132-1.44210.21691070.20692709X-RAY DIFFRACTION100
1.4421-1.47340.19471560.18472650X-RAY DIFFRACTION100
1.4734-1.50770.2041710.16882671X-RAY DIFFRACTION100
1.5077-1.54540.1551600.1522672X-RAY DIFFRACTION100
1.5454-1.58720.17311330.14822685X-RAY DIFFRACTION100
1.5872-1.63390.161380.13982679X-RAY DIFFRACTION100
1.6339-1.68660.1621230.13362716X-RAY DIFFRACTION100
1.6866-1.74690.12251110.13262732X-RAY DIFFRACTION100
1.7469-1.81690.1851310.13362704X-RAY DIFFRACTION100
1.8169-1.89960.14721470.12912703X-RAY DIFFRACTION100
1.8996-1.99970.13861410.11752705X-RAY DIFFRACTION100
1.9997-2.1250.12171440.11742706X-RAY DIFFRACTION100
2.125-2.28910.13851250.12382753X-RAY DIFFRACTION100
2.2891-2.51940.14971540.12572739X-RAY DIFFRACTION100
2.5194-2.8840.1461560.13222748X-RAY DIFFRACTION100
2.884-3.63330.14841470.12892777X-RAY DIFFRACTION100
3.6333-49.88020.17781540.15392913X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -39.9383 Å / Origin y: 13.3208 Å / Origin z: 98.6075 Å
111213212223313233
T0.1089 Å20.0024 Å20.0037 Å2-0.1054 Å20.0104 Å2--0.1108 Å2
L0.5733 °20.1841 °2-0.0143 °2-0.8792 °20.4876 °2--0.9149 °2
S-0.0124 Å °-0.0024 Å °-0.0411 Å °-0.0111 Å °0.0306 Å °-0.0232 Å °-0.0019 Å °0.0241 Å °0.0011 Å °
Refinement TLS groupSelection details: all

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